From Tor Ticket #8222 :
"Check certificates using tor for anonymity" should really be "only
check certificates using Tor for anonymity". If it's unchecked, it
means the observatory will use a direct SSL connection if it cannot
find Tor.
That option will be greyed out if HTTPS Everywhere failed to
successfully identify a method for making requests through Tor when it
started. But if Tor is installed or running or works correctly on a
future browser startup, the observatory will switch to using Tor at
that time, even if this option is unchecked.
This option should then be available and not greyed-out when Tor is running.
If that is not the case, update to the latest Tor and Tor browser versions,
and if this still arrives, then you could open a new support ticket.
However, you are safe even when the option is greyed, since the communication
with the EFF is encrypted.
As far as I know, the Tor browser already contains HTTPS Everywhere
and SSL Observatory, so you do not need to install the Firefox add-on.
SSL Observatory is off by default though.